Conformation superposition

Eor scoring of mapping quality, MOE simply uses the RMSD calculated for the model-conformer superposition. Thus, contrary to DS CATALYST, a low score corresponds to a good alignment between model features and conformer features [20]. 

The classic approach to pharmacophore development has been through the visual analysis of low-energy ligand conformer superpositions using molecular modeling packages. The work undertaken by Bures et al. to design new inhibitors of auxin transport provides an excellent example of the use of... 

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

Fig. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

IR spectroscopy is an inherently faster method than NMR and an IR spectrum is a superposition of the spectra of the various conformations rather than an average of them When 1 2 dichloroethane is cooled below its freezing point the crystalline matenal gives an IR spectrum consistent with a single species that has a center of symmetry At room temperature the IR spec trum of liquid 1 2 dichloroethane retains the peaks present in the solid but includes new peaks as well Explain these observations... 

Configurational energy for clathrates, 12 Configurations, superposition of, 258 Conformal solution theory, 137 Coordination polymerization, 148, 162, 170... 

In conformity with the superposition principle ( is a linear operator), the stability of the Cauchy problem with respect to the right-hand side follows from the uniform stability with respect to the initial data... 

The crystal structures of PbTX-1 dimethyl acetal, PbTX-1, and dihydro PbTX-1 provide a total of four independent pictures of the same brevetoxin skeleton. It is rare that this quantity of structural data is available for a natural product of this size. A comparison of torsional angles shows that all four molecules have approximately the same conformations in all rings, except, of course, for the aldehyde side chain and the E-ring in one of the independent molecules of PbTX-1. Least squares superposition fits among the four molecules gave the following average distances ... 

Because the time scale of the Raman scattering event ( 3.3 x 10-14s for a vibration with wavenumber shift 1000 cm-1 excited in the visible) is much shorter than that of the fastest conformational fluctuations in biomolecules, the ROA spectrum is a superposition of snapshot spectra from all the distinct chiral conformers present in the sample. Together with the dependence of ROA on chirality, this leads to an enhanced sensitivity to the dynamic aspects of biomolecular structure. The two-group model provides a qualitative explanation since it predicts ROA intensities that depend on absolute chirality in the form of a sin x dependence... 

The ROA spectra of partially unfolded denatured hen lysozyme and bovine ribonuclease A, prepared by reducing all the disulfide bonds and keeping the sample at low pH, together with the ROA spectra of the corresponding native proteins, are displayed in Figure 5. As pointed out in Section II,B, the short time scale of the Raman scattering event means that the ROA spectrum of a disordered system is a superposition of snapshot ROA spectra from all the distinct conformations present at equilibrium. Because of the reduced ROA intensities and large... 

Figure 9.24 shows temperature-reduced plots of 2d, Nc and 5 versus Tf + ATg. All the data conform well to a reduced curve like Figure 9.23. Interestingly, when the authors used both Tg and the melting temperature (Tm) [61] depressions to conduct superposition, they recognized that the reduced curve is nicely constructed but there is no significant difference compare with the case of Tf+ ATg. This indicates that Tg depression is important in optimizing foam processing conditions but Tm depression is not a significant factor for processing because the Tf range is still below Tm after C02 saturation.

A pharmacophore hypothesis can be derived from a series of known ligands and their common 3D-features. The pharmacophore is constructed by superimposing energetically favorable conformations of all ligands according to their consensus in structural features. The template structure for the superposition should fulfill two criteria ... 

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